Background: India has a third large population of people living with Human Immunodeficiency Virus (HIV) in the world. Incidence of Human papilloma virus (HPV) infection anal cancer is high among People Living with HIV/AIDS (PLHIV). However, there are very few studies among HIV positive men in India. Thus this cross-sectional study was performed to assess the prevalence and risk factors of anal HPV infection and anal HPV types in HIV positive males attending the Antiretroviral therapy (ART) centre. Methods & Materials: We screened HIV positive men with Anal Papanicolaou smear cytology and HPV testing. HPV DNA was detected by Consensus Polymerase Chain Reaction (PCR) using dissimilar E6 consensus and MY09/11 consensus primers followed by sequencing for confirmation the type of HPV. Results: 126 HIV-positive men were included in the study. Mean age was 35.37 ± 8.2 years. Median CD4+T cell counts were 253/μL. Mean weight and mean Hemoglobin was 49.53 ± 8.45 Kg and 11.2 ± 1.73 g/dl respectively.74 patients were treatment naive and 52 were on Anti-Retroviral Therapy (ART) 48 (38%) gave positive for history of anal intercourse with other men although 91% were married. Anal cytology was done in 95 patients, out of which 61(64.2%) had cytological abnormalities, of which 28 (29.4%) cases had LSIL, 33(34.7%), had ASCUS. In multivariate analysis, an only risk factor for cytological abnormality was a history of anal intercourse Odds Ratio (OR) 0.122 (95% 0.036-0.410).HPV DNA was detected in 27.5% patients. After sequencing, HPV-16 most prevalent HPV type in the study group was, identified in (10%, 12/120) followed by HPV-31 (4.1%, 5/120), HPV-35 (3.33%, 4/120) HPV-18 (2.5%, 3/120), HPV17, HPV-52, HPV-72 (1.2% each, 2/120) and HPV-66, HPV-68, HPV-107 (0.83% each, 3/120). Conclusion: In our study, the prevalence of HPV infection was 27.5% and anal cytological abnormality was 64.2% which is high. Anal Pap smear screening should be done especially in HIV positive males with the history of bisexuality.